Finite volume schemes for dispersive wave propagation and runup

Finite volume schemes are commonly used to construct approximate solutions to conservation laws. In this study we extend the framework of the finite volume methods to dispersive water wave models, in particular to Boussinesq type systems. We focus mainly on the application of the method to bidirectional nonlinear, dispersive wave propagation in one space dimension. Special emphasis is given to important nonlinear phenomena such as solitary waves interactions, dispersive shock wave formation and the runup of breaking and non-breaking long waves.Comment: 41 pafes, 20 figures. Other author's papers can be downloaded at http://www.lama.univ-savoie.fr/~dutykh

Network equilibration and first-principles liquid water.

Motivated by the very low diffusivity recently found in ab initio simulations of liquid water, we have studied its dependence with temperature, system size, and duration of the simulations. We use ab initio molecular dynamics (AIMD), following the Born-Oppenheimer forces obtained from density-functional theory (DFT). The linear-scaling capability of our method allows the consideration of larger system sizes (up to 128 molecules in this study), even if the main emphasis of this work is in the time scale. We obtain diffusivities that are substantially lower than the experimental values, in agreement with recent findings using similar methods. A fairly good agreement with D(T) experiments is obtained if the simulation temperature is scaled down by approximately 20%. It is still an open question whether the deviation is due to the limited accuracy of present density functionals or to quantum fluctuations, but neither technical approximations (basis set, localization for linear scaling) nor the system size (down to 32 molecules) deteriorate the DFT description in an appreciable way. We find that the need for long equilibration times is consequence of the slow process of rearranging the H-bond network (at least 20 ps at AIMDs room temperature). The diffusivity is observed to be very directly linked to network imperfection. This link does not appear an artifact of the simulations, but a genuine property of liquid water

Optimized Analytical Procedures for the Untargeted Metabolomic Profiling of Human Urine and Plasma by Combining Hydrophilic Interaction (HILIC) and Reverse-Phase Liquid Chromatography (RPLC)-Mass Spectrometry.

Profiling of body fluids is crucial for monitoring and discovering metabolic markers of health and disease and for providing insights into human physiology. Since human urine and plasma each contain an extreme diversity of metabolites, a single liquid chromatographic system when coupled to mass spectrometry (MS) is not sufficient to achieve reasonable metabolome coverage. Hydrophilic interaction liquid chromatography (HILIC) offers complementary information to reverse-phase liquid chromatography (RPLC) by retaining polar metabolites. With the objective of finding the optimal combined chromatographic solution to profile urine and plasma, we systematically investigated the performance of five HILIC columns with different chemistries operated at three different pH (acidic, neutral, basic) and five C18-silica RPLC columns. The zwitterionic column ZIC-HILIC operated at neutral pH provided optimal performance on a large set of hydrophilic metabolites. The RPLC columns Hypersil GOLD and Zorbax SB aq were proven to be best suited for the metabolic profiling of urine and plasma, respectively. Importantly, the optimized HILIC-MS method showed excellent intrabatch peak area reproducibility (CV < 12%) and good long-term interbatch (40 days) peak area reproducibility (CV < 22%) that were similar to those of RPLC-MS procedures. Finally, combining the optimal HILIC- and RPLC-MS approaches greatly expanded metabolome coverage with 44% and 108% new metabolic features detected compared with RPLC-MS alone for urine and plasma, respectively. The proposed combined LC-MS approaches improve the comprehensiveness of global metabolic profiling of body fluids and thus are valuable for monitoring and discovering metabolic changes associated with health and disease in clinical research studies

Method for coregistration of optical measurements of breast tissue with histopathology : the importance of accounting for tissue deformations

For the validation of optical diagnostic technologies, experimental results need to be benchmarked against the gold standard. Currently, the gold standard for tissue characterization is assessment of hematoxylin and eosin (H&E)-stained sections by a pathologist. When processing tissue into H&E sections, the shape of the tissue deforms with respect to the initial shape when it was optically measured. We demonstrate the importance of accounting for these tissue deformations when correlating optical measurement with routinely acquired histopathology. We propose a method to register the tissue in the H&E sections to the optical measurements, which corrects for these tissue deformations. We compare the registered H&E sections to H&E sections that were registered with an algorithm that does not account for tissue deformations by evaluating both the shape and the composition of the tissue and using microcomputer tomography data as an independent measure. The proposed method, which did account for tissue deformations, was more accurate than the method that did not account for tissue deformations. These results emphasize the need for a registration method that accounts for tissue deformations, such as the method presented in this study, which can aid in validating optical techniques for clinical use. (C) The Authors. Published by SPIE under a Creative Commons Attribution 4.0 Unported License

Nonequilibrium thermodynamics of interacting tunneling transport: variational grand potential, density-functional formulation, and nature of steady-state forces

The standard formulation of tunneling transport rests on an open-boundary modeling. There, conserving approximations to nonequilibrium Green function or quantum-statistical mechanics provide consistent but computational costly approaches; alternatively, use of density-dependent ballistic-transport calculations [e.g., Phys. Rev. B 52, 5335 (1995)], here denoted `DBT', provide computationally efficient (approximate) atomistic characterizations of the electron behavior but has until now lacked a formal justification. This paper presents an exact, variational nonequilibrium thermodynamic theory for fully interacting tunneling and provides a rigorous foundation for frozen-nuclei DBT calculations as a lowest order approximation to an exact nonequilibrium thermodynamics density functional evaluation. The theory starts from the complete electron nonequilibrium quantum statistical mechanics and I identify the operator for the nonequilibrium Gibbs free energy. I demonstrate a minimal property of a functional for the nonequilibrium thermodynamic grand potential which thus uniquely identifies the solution as the exact nonequilibrium density matrix. I also show that a uniqueness-of-density proof from a closely related study [Phys. Rev. B 78, 165109 (2008)] makes it possible to provide a single-particle formulation based on universal electron-density functionals. I illustrate a formal evaluation of the thermodynamics grand potential value which is closely related to the variation in scattering phase shifts and hence to Friedel density oscillations. This paper also discusses the difference between the here-presented exact thermodynamics forces and the often-used electrostatic forces. Finally the paper documents an inherent adiabatic nature of the thermodynamics forces and observes that these are suited for a nonequilibrium implementation of the Born-Oppenheimer approximation.Comment: 37 pages, 3 Figure

Coarse-grained simulation of amphiphilic self-assembly

We present a computer simulation study of amphiphilic self assembly performed using a computationally efficient single-site model based on Gay-Berne and Lennard-Jones particles. Molecular dynamics simulations of these systems show that free self-assembly of micellar, bilayer and inverse micelle arrangements can be readily achieved for a single model parameterisation. This self-assembly is predominantly driven by the anisotropy of the amphiphile-solvent interaction, amphiphile-amphiphile interactions being found to be of secondary importance. While amphiphile concentration is the main determinant of phase stability, molecular parameters such as headgroup size and interaction strength also have measurable affects on system properties. </p

Coherent Backscattering of light in a magnetic field

This paper describes how coherent backscattering is altered by an external magnetic field. In the theory presented, magneto-optical effects occur inside Mie scatterers embedded in a non-magnetic medium. Unlike previous theories based on point-like scatterers, the decrease of coherent backscattering is obtained in leading order of the magnetic field using rigorous Mie theory. This decrease is strongly enhanced in the proximity of resonances, which cause the path length of the wave inside a scatterer to be increased. Also presented is a novel analysis of the shape of the backscattering cone in a magnetic field.Comment: 27 pages, 5 figures, Revtex, to appear in Phys. Rev.

Water Scarcity in the Zambezi Basin in the Long-Term Future: A Risk Assessment

The aim of this paper is to explore possible futures for the Zambezi basin and to estimate the risks of different water management strategies. Existing uncertainties are translated into alternative assumptions. The risk of a certain management strategy, which has been developed under a given set of assumptions, is analysed by applying alternative assumptions. For the exploration of possible futures, a dynamic simulation model is used. Three ‘utopias’ and a number of ‘dystopias’ are considered. A utopia is based on a coherent set of assumptions with respect to world-view (how does the world function), management style (how do people respond) and context (exogenous developments). A dystopia evolves if some assumptions are taken differently. Using the risk assessment method described, the paper reflects on the water policy priorities earlier proposed in an expert meeting held in Harare. It is shown that in only one out of the nine cases putting the ‘Harare priorities’ into practice will work out effectively and without large tradeoffs. It is concluded that minimising risks would require a radical shift from supply towards demand policy.\u